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Fundamental and Computational Sciences Directorate

Staff information

Carrie Nicora

Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-02
Richland, WA 99352

PNNL Publications


  • Boiteau RM, DW Hoyt, CD Nicora, HA Kinmonth-Schultz, JK Ward, and AK Bingol. 2018. "Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction." Metabolites 8(1):Article No. 8.  doi:10.3390/metabo8010008
  • Menachery VD, A Schafer, KE Burnum-Johnson, HD Mitchell, AJ Eisfeld-Fenney, KB Walters, CD Nicora, SO Purvine, CP Casey, ME Monroe, KK Weitz, KG Stratton, BJM Webb-Robertson, L Gralinski, TO Metz, RD Smith, KM Waters, AC Sims, Y Kawaoka, and R Baric. 2018. "MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape." Proceedings of the National Academy of Sciences of the United States of America 115(5):E1012-E1021.  doi:10.1073/pnas.1706928115
  • Nicora CD, KE Burnum-Johnson, ES Nakayasu, CP Casey, RA White, III, T Roy Chowdhury, JE Kyle, YM Kim, RD Smith, TO Metz, JK Jansson, and EM Baker. 2018. "The MPLEx Protocol for Multi-Omic Analyses of Soil Samples." Journal of Visualized Experiments e57343(135):, doi:10.3791/57343


  • Boenisch MJ, KL Broz, SO Purvine, WB Chrisler, CD Nicora, L Connolly, M Freitag, SE Baker, and HC Kistler. 2017. "Structural reorganization of the fungal endoplasmic reticulum upon induction of mycotoxin biosynthesis." Scientific Reports 7:Article No. 44296.  doi:10.1038/srep44296
  • Booker AE, M Borton, R Daly, S Welch, CD Nicora, DW Hoyt, T Wilson, SO Purvine, R Wolfe, S Sharma, PJ Mouser, DR Cole, MS Lipton, KC Wrighton, and MJ Wilkins. 2017. "Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales." mSphere 2:Article No. e00257-17.  doi:10.1128/mSphereDirect.00257-17
  • Bryant A, MJ Aldape, CR Bayer, EJ Katahira, L Bond, CD Nicora, TL Fillmore, TRW Clauss, TO Metz, BJM Webb-Robertson, and DL Stevens. 2017. "Effects of delayed NSAID administration after experimental eccentric contraction injury - A cellular and proteomics study." PLoS One 12(12):Article No. e0172486.  doi:10.1371/journal.pone.0172486
  • Burnum-Johnson KE, JE Kyle, AJ Eisfeld, CP Casey, KG Stratton, JF Gonzalez, F Habyarimana, NM Negretti, AC Sims, S Chauhan, LB Thackray, P Halfmann, KB Walters, YM Kim, EM Zink, CD Nicora, KK Weitz, BJM Webb-Robertson, ES Nakayasu, B Ahmer, M Konkel, VL Motin, R Baric, MS Diamond, Y Kawaoka, KM Waters, RD Smith, and TO Metz. 2017. "MPLEx: A method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling." Analyst 142(3):442-448.  doi:10.1039/c6an02486f
  • Kerkhoven EJ, YM Kim, S Wei, CD Nicora, TL Fillmore, SO Purvine, BJM Webb-Robertson, RD Smith, SE Baker, TO Metz, and JB Nielsen. 2017. "Leucine biosynthesis is involved in regulating high lipid accumulation in Yarrowia lipolytica." mBio 8(3):Article No. e00857-17.  doi:10.1128/mBio.00857-17
  • Li M, Y Gao, W Qian, L Shi, Y Liu, WC Nelson, CD Nicora, CT Resch, CJ Thompson, S Yan, JK Fredrickson, JM Zachara, and C Liu. 2017. "Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes." Environmental Microbiology Reports 9(5):512-521.  doi:10.1111/1758-2229.12558
  • Liberton ML, WB Chrisler, CD Nicora, RJ Moore, RD Smith, DW Koppenaal, HB Pakrasi, and JM Jacobs. 2017. "Phycobilisome Truncation Causes Widespread Proteome Changes in Synechocystis sp. PCC 6803." PLoS One 12(3):e0173251.  doi:10.1371/journal.pone.0173251
  • Shi T, SI Quek, Y Gao, CD Nicora, S Nie, TL Fillmore, T Liu, KD Rodland, RD Smith, R Leach, IM Thompson, EA Vitello, WJ Ellis, AY Liu, and W Qian. 2017. "Multiplexed targeted mass spectrometry assays for prostate cancer-associated urinary proteins." Oncotarget 8(60):101887-101898.  doi:10.18632/oncotarget.21710
  • Solden L, DW Hoyt, WB Collins, JE Plank, R Daly, E Hildebrand, TJ Beavers, R Wolfe, CD Nicora, SO Purvine, M Carstensen, MS Lipton, DE Spalinger, JL Firkins, BA Wolfe, and KC Wrighton. 2017. "New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11." The ISME Journal 11(3):691-703.  doi:10.1038/ismej.2016.150


  • Ahmad R, CD Nicora, AK Shukla, RD Smith, W Qian, and AY Liu. 2016. "An efficient method for native protein purification in the selected range from prostate cancer tissue digests." Chinese Clinical Oncology 5(6):78.  doi:10.21037/cco.2016.12.03
  • Hiras J, YW Wu, K Deng, CD Nicora, JT Aldrich, D Frey, S Kolinko, EW Robinson, JM Jacobs, P Adams, TR Northen, BA Simmons, and SW Singer. 2016. "Comparative community proteomics demonstrates the unexpected importance of an actinobacterial glycoside hydrolase family 12 protein for crystalline cellulose hydrolysis." mBio 7(4):Article No. e01106-16.  doi:10.1128/mBio.01106-16
  • Khadempour L, KE Burnum-Johnson, ES Baker, CD Nicora, BJM Webb-Robertson, RA White, III, ME Monroe, EL Huang, RD Smith, and CR Currie. 2016. "The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates." Molecular Ecology 25(22):5795-5805.  doi:10.1111/mec.13872
  • Nakayasu ES, CD Nicora, AC Sims, KE Burnum-Johnson, YM Kim, JE Kyle, MM Matzke, AK Shukla, RK Chu, AA Schepmoes, JM Jacobs, R Baric, BJM Webb-Robertson, RD Smith, and TO Metz. 2016. "MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses." mSystems 1(3):e00043-16.  doi:10.1128/mSystems.00043-16
  • Pomraning KR, YM Kim, CD Nicora, RK Chu, EL Bredeweg, SO Purvine, D Hu, TO Metz, and SE Baker. 2016. "Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica." BMC Genomics 17(138):1-18.  doi:10.1186/s12864-016-2471-2
  • Shi T, M Niepel, JE McDermott, Y Gao, CD Nicora, WB Chrisler, LM Markillie, VA Petyuk, RD Smith, KD Rodland, P Sorger, W Qian, and HS Wiley. 2016. "Conservation of Protein Abundance Patterns Reveals the Regulatory Architecture of the of the EGFR-MAPK Pathway." Science Signaling 9(436):rs6.  doi:10.1126/scisignal.aaf0891
  • Sigdel TK, Y Gao, J He, A Wang, CD Nicora, TL Fillmore, T Shi, BJM Webb-Robertson, RD Smith, W Qian, O Salvatierra, DG Camp, II, and M Sarwal. 2016. "Mining the Human Urine Proteome for Monitoring Renal Transplant Injury ." Kidney International 89(6):1244-1252.  doi:10.1016/j.kint.2015.12.049
  • Smith D, CD Nicora, P Carini, MS Lipton, AD Norbeck, RD Smith, and SJ Giovannoni. 2016. "Proteome Remodeling in Response to Sulfur Limitation in “Candidatus Pelagibacter ubique”." mSystems 1(4):e00068-16.  doi:10.1128/mSystems.00068-16
  • Sun J, JD Todd, JC Thrash, Y Qian, MC Qian, B Temperton, J Guo, EMK Fowler, JT Aldrich, CD Nicora, MS Lipton, RD Smith, P De Leenheer, SH Payne, AW Johnston, CL Davie-Martin, KH Halsey, and SJ Giovannoni. 2016. "The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol." Nature Microbiology 1(8):Article No. 16065.  doi:10.1038/nmicrobiol.2016.65
  • Tisoncik-Go J, DJ Gasper, JE Kyle, AJ Eisfeld, C Selinger, M Hatta, J Morrison, MJ Korth, EM Zink, YM Kim, AA Schepmoes, CD Nicora, SO Purvine, KK Weitz, X Peng, R Green, SC Tilton, BJM Webb-Robertson, KM Waters, TO Metz, RD Smith, Y Kawaoka, M Suresh, L Josset, and MG Katze. 2016. "Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism." Cell Host & Microbe 19(2):254-66.  doi:10.1016/j.chom.2016.01.002
  • Walker LR, DW Hoyt, SM Walker, JK Ward, CD Nicora, and AK Bingol. 2016. "Unambiguous Metabolite Identification in High-throughput Metabolomics by Hybrid 1D 1H NMR/ESI MS1 Approach." Magnetic Resonance in Chemistry 54(12):998-1003.  doi:10.1002/mrc.4503
  • White RA, III, EM Bottos, T Roy Chowdhury, JD Zucker, CJ Brislawn, CD Nicora, SJ Fansler, KR Glaesemann, KA Glass, and JK Jansson. 2016. "Moleculo long-read sequencing facilitates assembly and resolves functionally active genomic bins from complex soil metagenomes." mSystems 1(3):, doi:10.1128/mSystems.00045-16


  • Aylward FO, L Khadempour, D Tremmel, BR McDonald, CD Nicora, S Wu, RJ Moore, DJ Orton, ME Monroe, PD Piehowski, SO Purvine, RD Smith, MS Lipton, KE Burnum-Johnson, and CR Currie. 2015. "Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants." PLoS One 10(8):e0134752.  doi:10.1371/journal.pone.0134752
  • Bernstein HC, MA Charania, RS McClure, NC Sadler, MR Melnicki, EA Hill, LM Markillie, CD Nicora, AT Wright, MF Romine, and AS Beliaev. 2015. "Multi-omic Dynamics Associate Oxygenic Photosynthesis with Nitrogenase-mediated H2 production in Cyanothece sp. ATCC 51142." Scientific Reports 5:Article No. 16004.  doi:10.1038/srep16004
  • Ream TS, JR Haag, F Pontvianne, CD Nicora, AD Norbeck, L Pasa-Tolic, and CS Pikaard. 2015. "Subunit compositions of Arabidopsis RNA polymerases I and III reveal Pol I- and Pol III- specific forms of the AC40 subunit, and alternative C53 subunits ." Nucleic Acids Research 43(8):4163-4178.  doi:10.1093/nar/gkv247
  • Sigdel TK, Y NG, S Lee, CD Nicora, W Qian, RD Smith, DG Camp, II, and MM Sarwal. 2015. "Perturbations in the Urinary Exosome in Transplant Rejection." Frontiers of Medicine 1:Article No. 57.  doi:10.3389/fmed.2014.00057
  • Touchette MH, GR Bommineni, RJ Delle Bovi, J Gadbery, CD Nicora, AK Shukla, JE Kyle, TO Metz, DW Martin, NS Sampson, WT Miller, PJ Tonge, and JC Seeliger. 2015. "Diacyltransferase Activity and Chain Length Specificity of Mycobacterium tuberculosis PapA5 in the Synthesis of Alkyl ß-Diol Lipids." Biochemistry 54(35):5457-5468.  doi:10.1021/acs.biochem.5b00455


  • Aryal UK, SJ Callister, BH McMahon, LA McCue, JN Brown, J Stockel, ML Liberton, S Mishra, X Zhang, CD Nicora, TE Angel, DW Koppenaal, RD Smith, HB Pakrasi, and LA Sherman. 2014. "Proteomic profiles of five strains of oxygenic photosynthetic cyanobacteria of the genus Cyanothece." Journal of Proteome Research 13(7):3262-3276.  doi:10.1021/pr5000889
  • Brown JN, HM Brewer, CD Nicora, KK Weitz, MJ Morris, AJ Skabelund, JN Adkins, RD Smith, JH Cho, and R Gelinas. 2014. "Protein and microRNA biomarkers from lavage, urine, and serum in military personnel evaluated for dyspnea." BMC Medical Genomics 7:Article No. 58.  doi:10.1186/1755-8794-7-58
  • Haag JR, B Brower-Toland, EK Krieger, L Sidorenko, CD Nicora, AD Norbeck, A Irsigler, H LaRue, J Brzeski, KA Mcginnis, S Ivashuta, L Pasa-Tolic, VL Chandler, and CS Pikaard. 2014. "Functional Diversification of Maize RNA Polymerase IV and V subtypes via Alternative Catalytic Subunits." Cell Reports 9(1):378-390.  doi:10.1016/j.celrep.2014.08.067
  • Huang EL, FO Aylward, YM Kim, BJM Webb-Robertson, CD Nicora, Z Hu, TO Metz, MS Lipton, RD Smith, CR Currie, and KE Burnum-Johnson. 2014. "The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation." Environmental Microbiology Reports 6(4):389-95.  doi:10.1111/1758-2229.12163
  • Mudenda L, S Aguilar Pierle, JE Turse, GA Scoles, SO Purvine, CD Nicora, TRW Clauss, MW Ueti, WC Brown, and KA Brayton. 2014. "Proteomics informed by transcriptomics identifies novel secreted proteins in Dermacentor andersoni saliva." International Journal for Parasitology 44(13):1029-1037.  doi:10.1016/j.ijpara.2014.07.003
  • Shi T, Y Gao, MJ Gaffrey, CD Nicora, TL Fillmore, WB Chrisler, MA Gritsenko, C Wu, J He, KJ Bloodsworth, R Zhao, DG Camp, II, T Liu, KD Rodland, RD Smith, HS Wiley, and W Qian. 2014. "Sensitive Targeted Quantification of ERK Phosphorylation Dynamics and Stoichiometry in Human Cells without Affinity Enrichment." Analytical Chemistry 87(2):1103-1110.  doi:10.1021/ac503797x
  • Shi T, Y Gao, SI Quek, TL Fillmore, CD Nicora, D Su, R Zhao, KD Rodland, T Liu, RD Smith, DW Chan, DG Camp, II, AY Liu, and W Qian. 2014. "A highly sensitive targeted mass spectrometric assay for quantification of low-abundance AGR2 in human urine and serum." Journal of Proteome Research 13(2):875-882.  doi:10.1021/pr400912c
  • Sigdel TK, CD Nicora, SC Hsieh, H Dai, W Qian, DG Camp, II, and MM Sarwal. 2014. "Optimization for Peptide Sample Preparation for Urine Peptidomics." Clinical Proteomics 11:Article No. 7.  doi:10.1186/1559-0275-11-7
  • Sigdel TK, N Salomonis, CD Nicora, S Ryu, J He, V Dinh, DJ Orton, RJ Moore, SC Hsieh, H Dai, M Thien-Vu, W Xiao, RD Smith, W Qian, DG Camp, II, and MM Sarwal. 2014. "The Identification of Novel Potential Injury Mechanisms and Candidate Biomarkers in Renal Allograft Rejection by Quantitative Proteomics." Molecular & Cellular Proteomics. MCP 13(2):621-631.  doi:10.1074/mcp.M113.030577
  • Webb-Robertson BJM, MM Matzke, S Datta, SH Payne, J Kang, LM Bramer, CD Nicora, AK Shukla, TO Metz, KD Rodland, RD Smith, MF Tardiff, JE McDermott, JG Pounds, and KM Waters. 2014. "Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements." Molecular and Cellular Proteomics 13(12):3639-3646.  doi:10.1074/mcp.M113.030932
  • Wrighton KC, C Castelle, MJ Wilkins, LA Hug, I Sharon, BC Thomas, KM Handley, SW Mullin, CD Nicora, A Singh, MS Lipton, PE Long, KH Williams, and JF Banfield. 2014. "Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer." The ISME Journal 8(7):1452-1463.  doi:10.1038/ismej.2013.249


  • Aylward FO, KE Burnum-Johnson, SG Tringe, C Teiling, D Tremmel, J Moeller, JJ Scott, KW Barry, PD Piehowski, CD Nicora, S Malfatti, ME Monroe, SO Purvine, LA Goodwin, RD Smith, G Weinstock, N Gerardo, G Suen, MS Lipton, and CR Currie. 2013. "Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens." Applied and Environmental Microbiology 79(12):3770-3778.  doi:10.1128/AEM.03833-12
  • D'haeseleer P, JM Gladden, M Allgaier, P Chain, SG Tringe, S Malfatti, JT Aldrich, CD Nicora, EW Robinson, L Pasa-Tolic, P Hugenholtz, BA Simmons, and SW Singer. 2013. "Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass." PLoS One 8(7):e68465.  doi:10.1371/journal.pone.0068465
  • DeAngelis KM, D Sharma, R Varney, BA Simmons, NG Isern, LM Markillie, CD Nicora, AD Norbeck, RC Taylor, JT Aldrich, and EW Robinson. 2013. "Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1." Frontiers in Microbiology 4:Article No. 280. 
  • Isanapong J, S Hambright, AG Willis, A Boonmee, SJ Callister, KE Burnum-Johnson, L Pasa-Tolic, CD Nicora, JT Wertz, T Schmidt, and JL Rodrigues. 2013. "Development of an ecophysiological model for Diplosphaera colotermitum TAV2, a termite hindgut Verrucomicrobium." The ISME Journal 7(9):1803-1813.  doi:10.1038/ismej.2013.74
  • Nicora CD, BJ Anderson, SJ Callister, AD Norbeck, SO Purvine, JK Jansson, OU Mason, M David, DD Jurelevicius, RD Smith, and MS Lipton. 2013. "Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies ." Proteomics 13(18-19):2776-2785.  doi:10.1002/pmic.201300003
  • Robidart JC, SJ Callister, PF Song, CD Nicora, CG Wheat, and PR Girguis. 2013. "Characterizing Microbial Community and Geochemical Dynamics at Hydrothermal Vents Using Osmotically Driven Continuous Fluid Samplers." Environmental Science & Technology 47(9):4399-4407.  doi:10.1021/es3037302
  • Shi T, TL Fillmore, Y Gao, R Zhao, J He, AA Schepmoes, CD Nicora, C Wu, JL Chambers, RJ Moore, J Kagan, S Srivastava, AY Liu, KD Rodland, T Liu, DG Camp, II, RD Smith, and W Qian. 2013. "Long-Gradient Separations Coupled with Selected Reaction Monitoring for Highly Sensitive, Large Scale Targeted Protein Quantification in a Single Analysis." Analytical Chemistry 85(19):9196-9203.  doi:10.1021/ac402105s
  • Wilkins MJ, KC Wrighton, CD Nicora, KH Williams, LA McCue, KM Handley, CS Miller, L Giloteaux, AP Montgomery, DR Lovley, JF Banfield, PE Long, and MS Lipton. 2013. "Fluctuations in Species-Level Protein Expression Occur during Element and Nutrient Cycling in the Subsurface ." PLoS One 8(3):e57819.  doi:10.1371/journal.pone.0057819
  • Zhou J, RK Krovvidi, Y Gao, H Gao, BO Petritis, A De, C Miller-Graziano, PE Bankey, VA Petyuk, CD Nicora, TRW Clauss, RJ Moore, T Shi, JN Brown, A Kaushal, W Xiao, RW Davis, RV Maier, RG Tompkins, W Qian, DG Camp, II, and RD Smith. 2013. "Trauma-associated Human Neutrophil Alterations Revealed by Comparative Proteomics Profiling." Proteomics - Clinical Applications 7(7-8):571-583.  doi:10.1002/prca.201200109


  • Aryal UK, J Stockel, EA Welsh, MA Gritsenko, CD Nicora, DW Koppenaal, RD Smith, HB Pakrasi, and JM Jacobs. 2012. "Dynamic proteome analysis of Cyanothece sp. ATCC 51142 under constant light." Journal of Proteome Research 11(2):609-619.  doi:10.1021/pr200959x
  • Aylward FO, KE Burnum, JJ Scott, G Suen, SG Tringe, SM Adams, KW Barry, CD Nicora, PD Piehowski, SO Purvine, GJ Starrett, LA Goodwin, RD Smith, MS Lipton, and CR Currie. 2012. "Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens." The ISME Journal 6(9):1688-1701.  doi:10.1038/ismej.2012.10
  • Chauvigne-Hines LM, LN Anderson, HM Weaver, JN Brown, PK Koech, CD Nicora, BA Hofstad, RD Smith, MJ Wilkins, SJ Callister, and AT Wright. 2012. "Suite of Activity-Based Probes for Cellulose-Degrading Enzymes." Journal of the American Chemical Society 134(50):20521-20532.  doi:10.1021/ja309790w
  • Chauvin T, F Xie, T Liu, CD Nicora, F Yang, DG Camp, II, RD Smith, and KP Roberts. 2012. "A Systematic Analysis of a Deep Mouse Epididymal Sperm Proteome." Biology of Reproduction 87(6):Article No. 141.  doi:10.1095/biolreprod.112.104208
  • Haag JR, TS Ream, M Marasco, CD Nicora, AD Norbeck, L Pasa-Tolic, and CS Pikaard. 2012. "In vitro transcription activities of Pol IV, Pol V and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing." Molecular Cell 48(5):811-8.  doi:10.1016/j.molcel.2012.09.027
  • Zhou J, GP Dann, T Shi, L Wang, X Gao, D Su, CD Nicora, AK Shukla, RJ Moore, T Liu, DG Camp, II, RD Smith, and W Qian. 2012. "Simple Sodium Dodecyl Sulfate-Assisted Sample Preparation Method for LC-MS-based Proteomic Applications." Analytical Chemistry 84(6):2862-2867.  doi:10.1021/ac203394r


  • Burnum KE, SJ Callister, CD Nicora, SO Purvine, P Hugenholtz, F Warnecke, RH Scheffrahn, RD Smith, and MS Lipton. 2011. "Proteome Insights into the Symbiotic Relationship Between a Captive Colony of Nasutitermes corniger and its Hindgut Microbiome." The ISME Journal 5(1):161-164.  doi:10.1038/ismej.2010.97
  • Parnell JJ, SJ Callister, G Rompato, CD Nicora, L Pasa-Tolic, A Williamson, and ME Pfrender. 2011. "Time-course analysis of the Shewanella amazonensis SB2B proteome in response to sodium chloride shock." Scientific Reports 1:Article No. 25.  doi:10.1038/srep00025
  • Qian W, BO Petritis, CD Nicora, and RD Smith. 2011. "Trypsin-catalyzed oxygen-18 labeling for quantitative proteomics." Chapter 3 in Gel-Free Proteomics, Methods and Protocols: Methods in Molecular Biology, vol. 753, ed. K Gevaert and J Vandekerckhove, pp. 43-54.  Humana Press Inc., Totowa, NJ. 
  • Stockel J, JM Jacobs, TR Elvitigala, ML Liberton, EA Welsh, AD Polpitiya, MA Gritsenko, CD Nicora, DW Koppenaal, RD Smith, and HB Pakrasi. 2011. "Diurnal Rhythms Result in Significant Changes in the Cellular Protein Complement in the Cyanobacterium Cyanothece 51142." PLoS One 6(2):Article No.: e16680.  doi:10.1371/journal.pone.0016680
  • Wilkins MJ, SJ Callister, M Miletto, KH Williams, CD Nicora, DR Lovely, PE Long, and MS Lipton. 2011. "Development of a biomarker for Geobacter activity and strain composition; Proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI)." Microbial Biotechnology 4(1):55-63.  doi:10.1111/j.1751-7915.2010.00194.x


  • Angel TE, BJ Luft, X Yang, CD Nicora, DG Camp, II, JM Jacobs, and RD Smith. 2010. "Proteome Analysis of Borrelia burgdorferi Response to Environmental Change." PLoS One 5(11):Article No.: e13800.  doi:10.1371/journal.pone.0013800
  • Callister SJ, MJ Wilkins, CD Nicora, KH Williams, JF Banfield, N VerBerkmoes, RL Hettich, AL N'Guessan, P Mouser, H Elifantz, RD Smith, DR Lovley, MS Lipton, and PE Long. 2010. "Analysis of Biostimulated Microbial Communities from Two Field Experiments Reveals Temporal and Spatial Differences in Proteome Profiles." Environmental Science & Technology 44(23):8897-8903.  doi:10.1021/es101029f
  • Smith DP, JB Kitner, AD Norbeck, TRW Clauss, MS Lipton, MS Schwalbach, L Steindler, CD Nicora, RD Smith, and SJ Giovannoni. 2010. "Transcriptional and translational regulatory responses to iron limitation in the globally distributed marine bacterium Candidatus Pelagibacter ubique." PLoS One 5(5):Article Number: e10487. 


  • Henne KL, JE Turse, CD Nicora, MS Lipton, SL Tollaksen, C Lindberg, G Babbnig, CS Giometti, CN Nakatsu, DK Thompson, and A Konopka. 2009. "Global Proteomic Analysis of the Chromate Response in Arthrobacter sp strain FB24." Journal of Proteome Research 8(4)(Sp.Iss.SI):1704-16.  doi:10.1021/Pr800705f
  • Kim W, MW Silby, SO Purvine, JS Nicoll, KK Hixson, ME Monroe, CD Nicora, MS Lipton, and SB Levy. 2009. "Proteomic Detection of Non-Annotated Protein-Coding Genes in Pseudomonas fluorescens Pf0-1." PLoS One 4(12):Article Number: e8455.  doi:10.1371/journal.pone.0008455
  • Ream TS, JR Haag, AT Wierzbicki, CD Nicora, AD Norbeck, JK Zhu, G Hagen, TJ Guilfoyle, L Pasa-Tolic, and CS Pikaard. 2009. "Subunit Compositions of the RNA-Silencing Enzymes Pol IV and Pol V Reveal Their Origins as Specialized Forms of RNA Polymerase II ." Molecular Cell 33(2):192-203.  doi:doi:10.1016/j.molcel.2008.12.015
  • Ream TS, JR Haag, AT Wierzbicki, CD Nicora, AD Norbeck, JK Zhu, G Hagen, TJ Guilfoyle, L Pasa-Tolic, and CS Pikaard. 2009. "Subunit Compositions of the RNA-Silencing Enzymes Pol IV and Pol V Reveal Their Origins as Specialized Forms of RNA Polymerase II." Molecular Cell 33(2):192-203.  doi:10.1016/j.molcel.2008.12.015
  • Sowell SM, L Wilhelm, AD Norbeck, MS Lipton, CD Nicora, DF Barofsky, C carlson, RD Smith, and SJ Giovannoni. 2009. " Transport Functions Dominate the SAR11 Metaproteome at Low-Nutrient Extremes in the Sargasso Sea." The ISME Journal 3(1):93-105. 
  • Wilkins MJ, NC VerBerkmoes, KH Williams, SJ Callister, P Mouser, H Elifantz, AL N'Guessan, BC Thomas, CD Nicora, MB Shah, P Abraham, MS Lipton, DR Lovely, RL Hettich, PE Long, and JF Banfield. 2009. "Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation." Applied and Environmental Microbiology 75(20):6591-6599.  doi:10.1128/AEM.01064-09


  • Sowell SM, AD Norbeck, MS Lipton, CD Nicora, SJ Callister, RD Smith, DF Barofsky, and SJ Giovannoni. 2008. "Proteomic Analysis of Stationary Phase in the Marine Bacterium 'Candidatus Pelagibacter ubique'." Applied and Environmental Microbiology 74(13):4091-4100.  doi:10.1128/AEM.00599-08
  • Sowell SM, AD Norbeck, MS Lipton, CD Nicora, SJ Callister, RD Smith, DF Barofsky, and SJ Giovannoni. 2008. "Proteomic Analysis of Stationary Phase in the Marine Bacterium 'Candidatus Pelagibacter ubique'." Applied and Environmental Microbiology 74(13):4091-4100.  doi:10.1128/AEM.00599-08


  • Callister SJ, CD Nicora, X Zeng, JH Roh, M Dominguez, C Tavano, ME Monroe, S Kaplan, T Donohue, RD Smith, and MS Lipton. 2006. "Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes." Journal of Microbiological Methods 67(3):424-436.  doi:10.1016/j.mimet.2006.04.021
  • Callister SJ, M Dominguez, CD Nicora, X Zeng, C Tavano, S Kaplan, T Donohue, RD Smith, and MS Lipton. 2006. "Application of the Accurate Mass and Time Tag Approach to the Proteome Analysis of Sub-cellular Fractions Obtained from Rhodobacter sphaeroides 2.4.1 Aerobic and Photosynthetic Cell Cultures." Journal of Proteome Research 5(8):1940-1947. 
  • Fang R, DA Elias, ME Monroe, Y Shen, M McIntosh, P Wang, CD Goddard, SJ Callister, RJ Moore, YA Gorby, JN Adkins, JK Fredrickson, MS Lipton, and RD Smith. 2006. "Differential Label-free Quantitative Proteomic Analysis of Shewanella oneidensis Cultured under Aerobic and Suboxic Conditions by Accurate Mass and Time Tag Approach." Molecular & Cellular Proteomics. MCP 5(4):714-725.  doi:10.1074/mcp.M500301-MCP200
  • Yang F, DL Stenoien, EF Strittmatter, JH Wang, L Ding, MS Lipton, ME Monroe, CD Nicora, MA Gritsenko, K Tang, R Fang, JN Adkins, DG Camp, II, DJ Chen, and RD Smith. 2006. "Phosphoproteome Profiling of Human Skin Fibroplast Cells in Response to Low- and High-Dose Irradiation ." Journal of Proteome Research 5(5):1252-1260. 

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